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Step 1
Preheat: Position oven racks in the upper- and lower-thirds of oven. Preheat to 425℉ (220℃).
Step 2
Roast Veggies: Line two baking sheets with parchment. Spread 1½ lb cubed butternut squash on one sheet. Spread 1 large diced yellow onion and 3 cups chopped mushrooms on the other. Toss veggies with 1 tablespoon extra virgin olive oil to coat. Sprinkle with ½ teaspoon fine sea salt and ¼ teaspoon black pepper. Bake—with the butternut squash on the upper rack—until golden brown, about 25 minutes.
Step 3
Cook Pasta: Meanwhile, bring a large pot of salted water to boil. Cook 1 lb dried rigatoni pasta for 2 minutes less than al dente, according to package instructions. Drain the pasta.
Step 4
Make Breadcrumbs: Warm 1 tablespoon extra virgin olive oil in another large pot over medium-low heat. (Pot needs to be big enough to hold pasta and sauce). Stir in ⅓ cup panko breadcrumbs and ¼ cup chopped walnuts. Cook, stirring frequently, until golden, 4 to 6 minutes. Transfer to a small bowl and season with salt and pepper to taste.
Step 5
Start Sauce: Wipe out any crumbs from the pot. Warm 3 tablespoons extra virgin olive oil over medium heat. Add 4 cloves minced garlic and cook, stirring frequently, until garlic is golden, about 2 minutes. Sprinkle in ⅓ cup all purpose flour and stir to coat. Stir in 3 cups milk, 2 cups vegetable broth, 1 teaspoon dried sage, 1 tablespoon fresh thyme leaves, 1 teaspoon fine sea salt, and ¼ teaspoon black pepper. Let sauce come to a bubble, stirring occasionally. Then cook, stirring frequently, until the sauce thickens slightly to coat the back of a spoon, 1 to 3 minutes. Reduce heat to low.
Step 6
Combine: Add cooked pasta to the sauce. Stir to coat. Add 3 cups chopped kale and the roasted butternut squash, mushrooms, and onion. Stir well to mix. (It should be very saucy).
Step 7
Assemble and Bake: Combine 2 cups shredded aged cheddar and 1½ cups shredded mozzarella in a small bowl. Transfer half the pasta into a 9x13-inch (23x33 cm) casserole dish. Sprinkle with half the cheese. Layer remaining pasta, sauce, and lastly the cheese. Bake on the upper rack (see note until bubbling and golden brown, 10 to 15 minutes. Scatter walnut breadcrumbs on top and serve.